Adaptive Thermogenesis and Obesity

I'm sure that most proponents of the "calories in, calories out" theory of weight management would agree that energy expenditure plays a significant role in obesity. And I don't disagree.....but are most nutritionists and doctors looking at the wrong component of energy expenditure?
Total energy expenditure (or TEE), is the total amount of energy (i.e. calories) your body burns in a day. It is the sum of three distinct parts:
1) Obligatory energy expenditure - This is the energy required by the body to perform necessary cellular and organ functions.
2) Physical activity - Any additional energy burned by the body to fuel physical activity of any sort.
3) Adaptive thermogenesis - Additional energy expenditure induced by diet or cold exposure.
Most nutritionists and MD's believe that reduced physical activity is one of the root causes of obesity. Many also believe that reduced obligatory energy expenditure (i.e. "a slow metabolism") also contributes. But the picture looks very different once you look at the scientific literature.
In most animal studies, the difference between lean and obese subjuects is found in adaptive thermogenesis. In basic terms this means that most animals fed a high calorie diet do not gain weight. They off-set the increased calories by spontaneously increasing diet induced thermogenesis. With little exception, only when an abnormality in this process exists do animals gain weight. (1) Even when calorie intake and energy expenditure are equalized, some animals will gain weight while others remain lean.
Humans are much harder to study than rodents. But if human obesity is similar to rodent obesity (which is probable) it would help us to explore other reasons why our population is gaining so much weight. The typical "eat less and exercise more" treatment for obesity has failed, and abnormalities in diet induced thermogenesis is likely one of the culprits.
Is it possible that a diet high in refined carbohydrates and food toxins found in industrial foods (like wheat and seed oils) are interfering with our body's ability to adjust to normal fluctuations in energy intake? Could these same refined carbs and food toxins be disrupting natural hormonal feedback loops that regulate body fat stores? 
If this is the case, as I believe, the most effective treatment for obesity would be a natural diet of unprocessed foods such as vegetables, nuts, meat, poultry, seafood, and fruit. Short term restriction of all carbohydrates, even natural, healthful sources such as berries and sweet potatoes, would also likely be beneficial. 

References

1) "β-Adrenergic Receptors, Diet-induced Thermogenesis, and Obesity",

Bradford B. Lowell and 

Eric S. Bachman. Journal of Biochemistry, 278, 29385-29388.